[English] 日本語
Yorodumi
- PDB-5a5t: Structure of mammalian eIF3 in the context of the 43S preinitiati... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a5t
TitleStructure of mammalian eIF3 in the context of the 43S preinitiation complex
Components
  • (EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT ...) x 7
  • UNCHARACTERIZED PROTEIN
KeywordsHYDROLASE / EIF3 / EUKARYOTIC INITIATION FACTOR 3 / PREINITIATION COMPLEX / PCI/MPN CORE / EIF3G/I/B / EIF3D
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / protein deubiquitination / translation initiation factor binding / translation initiation factor activity / positive regulation of translation / PML body / fibrillar center / metallopeptidase activity / ribosome binding / cysteine-type deubiquitinase activity / postsynaptic density / mRNA binding / synapse / nucleolus / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit 6 N terminal domain / eIF3 subunit M, C-terminal helix ...Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit 6 N terminal domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / : / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit L / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit F
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
Authorsdes-Georges, A. / Dhote, V. / Kuhn, L. / Hellen, C.U.T. / Pestova, T.V. / Frank, J. / Hashem, Y.
CitationJournal: Nature / Year: 2015
Title: Structure of mammalian eIF3 in the context of the 43S preinitiation complex.
Authors: Amedee des Georges / Vidya Dhote / Lauriane Kuhn / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank / Yaser Hashem /
Abstract: During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of ...During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of messenger RNA and scan along it to the initiation codon. Scanning on structured mRNAs also requires the DExH-box protein DHX29. Mammalian eIF3 contains 13 subunits and participates in nearly all steps of translation initiation. Eight subunits having PCI (proteasome, COP9 signalosome, eIF3) or MPN (Mpr1, Pad1, amino-terminal) domains constitute the structural core of eIF3, to which five peripheral subunits are flexibly linked. Here we present a cryo-electron microscopy structure of eIF3 in the context of the DHX29-bound 43S complex, showing the PCI/MPN core at ∼6 Å resolution. It reveals the organization of the individual subunits and their interactions with components of the 43S complex. We were able to build near-complete polyalanine-level models of the eIF3 PCI/MPN core and of two peripheral subunits. The implications for understanding mRNA ribosomal attachment and scanning are discussed.
History
DepositionJun 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_image_scans
Revision 1.4Oct 3, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3056
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F
H: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H
K: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K
L: UNCHARACTERIZED PROTEIN
M: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M


Theoretical massNumber of molelcules
Total (without water)527,3978
Polymers527,3978
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

-
EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT ... , 7 types, 7 molecules ACEFHKM

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT A / EIF3A / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 10 / EIF-3-THETA


Mass: 164902.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1SMZ5
#2: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT C / EIF3C / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 8 / EIF3 P110


Mass: 97923.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1U971
#3: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E / EIF3E / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 6 / EIF-3 P48


Mass: 52281.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1SUC8
#4: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F / EIF3F / DEUBIQUITINATING ENZYME EIF3F / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 5 / EIF- ...EIF3F / DEUBIQUITINATING ENZYME EIF3F / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 5 / EIF-3-EPSILON / EIF3 P47


Mass: 37846.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: U3KNL5, ubiquitinyl hydrolase 1
#5: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H / EIF3H / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 3 / EIF-3-GAMMA / EIF3 P40 SUBUNIT


Mass: 39952.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1ST95
#6: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT K / EIF3K / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 12 / EIF-3 P25


Mass: 25129.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1T3L2
#8: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT M / EIF3M / FETAL LUNG PROTEIN B5 / HFL-B5 / PCI DOMAIN-CONTAINING PROTEIN 1


Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1SLW8

-
Protein , 1 types, 1 molecules L

#7: Protein UNCHARACTERIZED PROTEIN


Mass: 66804.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell line: RETICULCYTES / Tissue: BLOOD / References: UniProt: G1SED9

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: EIF3 OCTAMER CORE OF RABBIT EIF3 / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV,

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE / Date: Nov 1, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 30120 X / Nominal defocus max: 4500 nm / Nominal defocus min: 500 nm / Cs: 2 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)

-
Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: TEMPLATE MATCHING / Resolution: 6 Å / Num. of particles: 87192 / Actual pixel size: 1.66 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3056. (DEPOSITION ID: 13501).
Symmetry type: POINT
RefinementHighest resolution: 6 Å
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25432 0 0 0 25432

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more